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Volumn 168, Issue 6, 2011, Pages 611-618

Large cliques in Arabidopsis gene coexpression network and motif discovery

Author keywords

Arabidopsis; Cis regulatory elements; Gene coexpression network; Maximal cliques; Motif

Indexed keywords

ARABIDOPSIS PROTEIN; TRANSCRIPTION FACTOR;

EID: 79951767774     PISSN: 01761617     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jplph.2010.09.010     Document Type: Article
Times cited : (28)

References (45)
  • 1
    • 0036013593 scopus 로고    scopus 로고
    • Statistical mechanics of complex networks
    • Albert R., Barabási A.L. Statistical mechanics of complex networks. Rev Mod Phys 2002, 74:47-97.
    • (2002) Rev Mod Phys , vol.74 , pp. 47-97
    • Albert, R.1    Barabási, A.L.2
  • 2
    • 0025904136 scopus 로고
    • Finding maximum cliques in arbitrary and in special graphs
    • Babel L. Finding maximum cliques in arbitrary and in special graphs. Computing 1991, 46:321-341.
    • (1991) Computing , vol.46 , pp. 321-341
    • Babel, L.1
  • 3
    • 0028685490 scopus 로고
    • Fitting a mixture model by expectation maximization to discover motifs in biopolymers
    • Bailey T.L., Elkan C. Fitting a mixture model by expectation maximization to discover motifs in biopolymers. Proc Int Conf Intell Syst Mol Biol 1994, 2:28-36.
    • (1994) Proc Int Conf Intell Syst Mol Biol , vol.2 , pp. 28-36
    • Bailey, T.L.1    Elkan, C.2
  • 4
    • 0022808049 scopus 로고
    • Finding a maximum clique in an arbitrary graph
    • Balas E., Yu C.S. Finding a maximum clique in an arbitrary graph. SIAM J Comput 1986, 15(4):1054-1068.
    • (1986) SIAM J Comput , vol.15 , Issue.4 , pp. 1054-1068
    • Balas, E.1    Yu, C.S.2
  • 5
    • 0345874725 scopus 로고    scopus 로고
    • CONREAL: conserved regulatory elements anchored alignment algorithm for identification of transcription factor binding sites by phylogenetic footprinting
    • Berezikov E., Guryev V., Plasterk R.H.A., Cuppen E. CONREAL: conserved regulatory elements anchored alignment algorithm for identification of transcription factor binding sites by phylogenetic footprinting. Genome Res 2004, 14:170-178.
    • (2004) Genome Res , vol.14 , pp. 170-178
    • Berezikov, E.1    Guryev, V.2    Plasterk, R.H.A.3    Cuppen, E.4
  • 6
    • 33746616867 scopus 로고    scopus 로고
    • Cross-species analysis of biological networks by Bayesian alignment
    • Berg J., Lässig M. Cross-species analysis of biological networks by Bayesian alignment. Proc Natl Acad Sci USA 2006, 103(29):10967-10972.
    • (2006) Proc Natl Acad Sci USA , vol.103 , Issue.29 , pp. 10967-10972
    • Berg, J.1    Lässig, M.2
  • 8
    • 0642281348 scopus 로고    scopus 로고
    • Correlating overrepresented upstream motifs to gene expression: a computational approach to regulatory element discovery in eukaryotes
    • Caselle M., Di Cunto F., Provero P. Correlating overrepresented upstream motifs to gene expression: a computational approach to regulatory element discovery in eukaryotes. BMC Bioinformatics 2002, 3:7-16.
    • (2002) BMC Bioinformatics , vol.3 , pp. 7-16
    • Caselle, M.1    Di Cunto, F.2    Provero, P.3
  • 9
    • 0034919548 scopus 로고    scopus 로고
    • Surveying Saccharomyces genomes to identify functional elements by comparative DNA sequence analysis
    • Cliften P.F., Hillier L.W., Fulton L., Graves T., Miner T., Gish W.R., et al. Surveying Saccharomyces genomes to identify functional elements by comparative DNA sequence analysis. Genome Res 2001, 11:1175-1186.
    • (2001) Genome Res , vol.11 , pp. 1175-1186
    • Cliften, P.F.1    Hillier, L.W.2    Fulton, L.3    Graves, T.4    Miner, T.5    Gish, W.R.6
  • 10
    • 0038724989 scopus 로고    scopus 로고
    • Finding functional features in Saccharomyces genomes by phylogenetic footprinting
    • Cliften P., Sudarsanam P., Desikan A., Fulton L., Fulton B., Majors J., et al. Finding functional features in Saccharomyces genomes by phylogenetic footprinting. Science 2003, 301:71-76.
    • (2003) Science , vol.301 , pp. 71-76
    • Cliften, P.1    Sudarsanam, P.2    Desikan, A.3    Fulton, L.4    Fulton, B.5    Majors, J.6
  • 11
    • 38549144819 scopus 로고    scopus 로고
    • A survey of DNA motif finding algorithms
    • Das M., Dai H.K. A survey of DNA motif finding algorithms. BMC Bioinformatics 2007, 8(Suppl.7):S21.
    • (2007) BMC Bioinformatics , vol.8 , Issue.SUPPL.7
    • Das, M.1    Dai, H.K.2
  • 12
    • 0347492019 scopus 로고    scopus 로고
    • AGRIS: Arabidopsis gene regulatory information server, an information resource of Arabidopsis cis-regulatory elements and transcription factors
    • Davuluri R.V., Sun H., Palaniswamy S.K., Matthews N., Molina C., Kurtz M., et al. AGRIS: Arabidopsis gene regulatory information server, an information resource of Arabidopsis cis-regulatory elements and transcription factors. BMC Bioinformatics 2003, 4:25-36.
    • (2003) BMC Bioinformatics , vol.4 , pp. 25-36
    • Davuluri, R.V.1    Sun, H.2    Palaniswamy, S.K.3    Matthews, N.4    Molina, C.5    Kurtz, M.6
  • 13
    • 0018199224 scopus 로고
    • DNAse footprinting: a simple method for the detection of protein-DNA binding specificity
    • Galas D.J., Schmitz A. DNAse footprinting: a simple method for the detection of protein-DNA binding specificity. Nucleic Acids Res 1978, 5(9):3157-3170.
    • (1978) Nucleic Acids Res , vol.5 , Issue.9 , pp. 3157-3170
    • Galas, D.J.1    Schmitz, A.2
  • 14
    • 33845669975 scopus 로고    scopus 로고
    • Large-scale cis-element detection by analysis of correlated expression and sequence conservation between Arabidopsis and Brassica oleracea
    • Haberer G., Mader M.T., Kosarev P., Spannagl M., Yang L., Mayer K.F. Large-scale cis-element detection by analysis of correlated expression and sequence conservation between Arabidopsis and Brassica oleracea. Plant Physiol 2006, 142:1589-1602.
    • (2006) Plant Physiol , vol.142 , pp. 1589-1602
    • Haberer, G.1    Mader, M.T.2    Kosarev, P.3    Spannagl, M.4    Yang, L.5    Mayer, K.F.6
  • 15
    • 0032826179 scopus 로고    scopus 로고
    • Identifying DNA and protein patterns with statistically significant alignments of multiple sequences
    • Hertz G.Z., Stormo G.D. Identifying DNA and protein patterns with statistically significant alignments of multiple sequences. Bioinformatics 1999, 15:563-577.
    • (1999) Bioinformatics , vol.15 , pp. 563-577
    • Hertz, G.Z.1    Stormo, G.D.2
  • 16
    • 26444584579 scopus 로고    scopus 로고
    • Limitations and potentials of current motif discovery algorithms
    • Hu J., Li B., Kihara D. Limitations and potentials of current motif discovery algorithms. Nucleic Acids Res 2005, 33(15):4899-4913.
    • (2005) Nucleic Acids Res , vol.33 , Issue.15 , pp. 4899-4913
    • Hu, J.1    Li, B.2    Kihara, D.3
  • 17
    • 0034628901 scopus 로고    scopus 로고
    • Computational identification of cis-regulatory elements associated with groups of functionally related genes in Saccharomyces cerevisiae
    • Hughes J.D., Estep P.W., Tavazoie S., Church G.M. Computational identification of cis-regulatory elements associated with groups of functionally related genes in Saccharomyces cerevisiae. J Mol Biol 2000, 296(5):1205-1214.
    • (2000) J Mol Biol , vol.296 , Issue.5 , pp. 1205-1214
    • Hughes, J.D.1    Estep, P.W.2    Tavazoie, S.3    Church, G.M.4
  • 18
    • 77951744224 scopus 로고    scopus 로고
    • Random matrix analysis of localization properties of gene coexpression network
    • Jalan S., Solymosi N., Vattay G., Li B. Random matrix analysis of localization properties of gene coexpression network. Phys Rev E 2010, 81:046118.
    • (2010) Phys Rev E , vol.81 , pp. 046118
    • Jalan, S.1    Solymosi, N.2    Vattay, G.3    Li, B.4
  • 19
    • 6344241652 scopus 로고    scopus 로고
    • Conservation and coevolution in the scale-free human gene coexpression network
    • Jordan I.K., Marino-Ramirez L., Wolf Y.I., Koonin E.V. Conservation and coevolution in the scale-free human gene coexpression network. Mol Biol Evol 2004, 21(11):2058-2070.
    • (2004) Mol Biol Evol , vol.21 , Issue.11 , pp. 2058-2070
    • Jordan, I.K.1    Marino-Ramirez, L.2    Wolf, Y.I.3    Koonin, E.V.4
  • 20
    • 35348992193 scopus 로고    scopus 로고
    • An improved branch and bound algorithm for the maximum clique problem
    • Konc J., Janežič D. An improved branch and bound algorithm for the maximum clique problem. MATCH Commun Math Comput Chem 2007, 58:569-590.
    • (2007) MATCH Commun Math Comput Chem , vol.58 , pp. 569-590
    • Konc, J.1    Janežič, D.2
  • 21
    • 0027912333 scopus 로고
    • Detecting subtle sequence signals: a Gibbs sampling strategy for multiple alignment
    • Lawrence C., Altschul S., Boguski M., Liu J., Neuwald A., Wootton J. Detecting subtle sequence signals: a Gibbs sampling strategy for multiple alignment. Science 1993, 262:208-214.
    • (1993) Science , vol.262 , pp. 208-214
    • Lawrence, C.1    Altschul, S.2    Boguski, M.3    Liu, J.4    Neuwald, A.5    Wootton, J.6
  • 23
    • 0035228215 scopus 로고    scopus 로고
    • BioProspector: discovering conserved DNA motifs in upstream regulatory regions of co-expressed genes
    • Liu X., Brutlag D.L., Liu J.S. BioProspector: discovering conserved DNA motifs in upstream regulatory regions of co-expressed genes. Pac Symp Biocomput 2001, 127-138.
    • (2001) Pac Symp Biocomput , pp. 127-138
    • Liu, X.1    Brutlag, D.L.2    Liu, J.S.3
  • 24
    • 0036324753 scopus 로고    scopus 로고
    • An algorithm for finding protein-DNA binding sites with applications to chromatin immunoprecipitation microarray experiments
    • Liu X.S., Brutlag D.L., Liu J.S. An algorithm for finding protein-DNA binding sites with applications to chromatin immunoprecipitation microarray experiments. Nat Biotechnol 2002, 20(8):835-839.
    • (2002) Nat Biotechnol , vol.20 , Issue.8 , pp. 835-839
    • Liu, X.S.1    Brutlag, D.L.2    Liu, J.S.3
  • 25
    • 34547569191 scopus 로고    scopus 로고
    • STAMP: a web tool for exploring DNA-binding motif similarities
    • Mahony S., Benos P.V. STAMP: a web tool for exploring DNA-binding motif similarities. Nucleic Acids Res 2007, 35:W253-W258.
    • (2007) Nucleic Acids Res , vol.35
    • Mahony, S.1    Benos, P.V.2
  • 26
    • 71749094192 scopus 로고    scopus 로고
    • Arabidopsis gene co-expression network and its functional modules
    • Mao L., Hemert J.L.V., Dash S., Dickerson J.A. Arabidopsis gene co-expression network and its functional modules. BMC Bioinformatics 2009, 10:346-369.
    • (2009) BMC Bioinformatics , vol.10 , pp. 346-369
    • Mao, L.1    Hemert, J.L.V.2    Dash, S.3    Dickerson, J.A.4
  • 27
    • 33846061087 scopus 로고    scopus 로고
    • ATTED-II: a database of co-expressed genes and cis elements for identifying coregulated gene groups in Arabidopsis
    • Obayashi T., Kinoshita K., Nakai K., Shibaoka M., Hayashi S., Saeki M., et al. ATTED-II: a database of co-expressed genes and cis elements for identifying coregulated gene groups in Arabidopsis. Nucleic Acids Res 2007, 35:D863-D869.
    • (2007) Nucleic Acids Res , vol.35
    • Obayashi, T.1    Kinoshita, K.2    Nakai, K.3    Shibaoka, M.4    Hayashi, S.5    Saeki, M.6
  • 29
    • 0038579896 scopus 로고
    • The maximum clique problem
    • Pardalos P.M., Xue J. The maximum clique problem. J Global Optim 1994, 4:301-328.
    • (1994) J Global Optim , vol.4 , pp. 301-328
    • Pardalos, P.M.1    Xue, J.2
  • 30
    • 3242884167 scopus 로고    scopus 로고
    • Weeder Web: discovery of transcription factor binding sites in a set of sequences from coregulated genes
    • Pavesi G., Mereghetti P., Mauri G., Pesole G. Weeder Web: discovery of transcription factor binding sites in a set of sequences from coregulated genes. Nucleic Acids Res 2004, 32:W199-W203.
    • (2004) Nucleic Acids Res , vol.32
    • Pavesi, G.1    Mereghetti, P.2    Mauri, G.3    Pesole, G.4
  • 31
    • 34247579156 scopus 로고    scopus 로고
    • A survey of motif discovery methods in an integrated framework
    • Sandve G.K., Drabløs F. A survey of motif discovery methods in an integrated framework. Biol Dir 2006, 1:11-26.
    • (2006) Biol Dir , vol.1 , pp. 11-26
    • Sandve, G.K.1    Drabløs, F.2
  • 32
    • 13444278955 scopus 로고    scopus 로고
    • Genomic studies of transcription factor-DNA interactions
    • Sikder D., Kodadek T. Genomic studies of transcription factor-DNA interactions. Curr Opin Chem Biol 2005, 9:38-45.
    • (2005) Curr Opin Chem Biol , vol.9 , pp. 38-45
    • Sikder, D.1    Kodadek, T.2
  • 33
    • 0042905768 scopus 로고    scopus 로고
    • YMF: a program for discovery of novel transcription factor binding sites by statistical overrepresentation
    • Sinha S., Tompa M. YMF: a program for discovery of novel transcription factor binding sites by statistical overrepresentation. Nucleic Acids Res 2003, 31:3586-3588.
    • (2003) Nucleic Acids Res , vol.31 , pp. 3586-3588
    • Sinha, S.1    Tompa, M.2
  • 34
    • 0345863918 scopus 로고    scopus 로고
    • AthaMap: an online resource for in silico transcription factor binding sites in the Arabidopsis thaliana genome
    • Steffens N.O., Galuschka C., Schindler M., Bülow L., Hehl R. AthaMap: an online resource for in silico transcription factor binding sites in the Arabidopsis thaliana genome. Nucleic Acids Res 2004, 32:D368-D372.
    • (2004) Nucleic Acids Res , vol.32
    • Steffens, N.O.1    Galuschka, C.2    Schindler, M.3    Bülow, L.4    Hehl, R.5
  • 35
    • 0034072450 scopus 로고    scopus 로고
    • DNA binding sites: representation and discovery
    • Stormo G.D. DNA binding sites: representation and discovery. Bioinformatics 2000, 16:16-23.
    • (2000) Bioinformatics , vol.16 , pp. 16-23
    • Stormo, G.D.1
  • 36
    • 0141993704 scopus 로고    scopus 로고
    • A gene-coexpression network for global discovery of conserved genetic modules
    • Stuart J.M., Segal E., Koller D., Kim S.K. A gene-coexpression network for global discovery of conserved genetic modules. Science 2003, 302(5643):249-255.
    • (2003) Science , vol.302 , Issue.5643 , pp. 249-255
    • Stuart, J.M.1    Segal, E.2    Koller, D.3    Kim, S.K.4
  • 37
    • 0036137323 scopus 로고    scopus 로고
    • A higher order background model improves the detection of regulatory elements by Gibbs sampling
    • Thijs G., Lescot M., Marchal K., Rombauts S., De Moor B., Rouzé P., et al. A higher order background model improves the detection of regulatory elements by Gibbs sampling. Bioinformatics 2001, 17(12):1113-1122.
    • (2001) Bioinformatics , vol.17 , Issue.12 , pp. 1113-1122
    • Thijs, G.1    Lescot, M.2    Marchal, K.3    Rombauts, S.4    De Moor, B.5    Rouzé, P.6
  • 39
    • 21144439147 scopus 로고    scopus 로고
    • Assessing computational tools for the discovery of transcription factor binding sites
    • Tompa M., Li N., Bailey T.L., Church G.M., De Moor B., Eskin E., et al. Assessing computational tools for the discovery of transcription factor binding sites. Nat Biotechnol 2005, 23:137-144.
    • (2005) Nat Biotechnol , vol.23 , pp. 137-144
    • Tompa, M.1    Li, N.2    Bailey, T.L.3    Church, G.M.4    De Moor, B.5    Eskin, E.6
  • 40
    • 4644292576 scopus 로고    scopus 로고
    • The yeast coexpression network has a small-world, scale-free architecture and can be explained by a simple model
    • van Noort V., Snel B., Huynen M.A. The yeast coexpression network has a small-world, scale-free architecture and can be explained by a simple model. EMBO Rep 2004, 5:280-284.
    • (2004) EMBO Rep , vol.5 , pp. 280-284
    • van Noort, V.1    Snel, B.2    Huynen, M.A.3
  • 42
    • 66649122827 scopus 로고    scopus 로고
    • Unraveling transcriptional control in Arabidopsis using cis-regulatory elements and coexpression networks
    • Vandepoele K., Quimbaya M., Casneuf T., De Veylder L., Peer Van de Y. Unraveling transcriptional control in Arabidopsis using cis-regulatory elements and coexpression networks. Plant Physiol 2009, 150(2):535-546.
    • (2009) Plant Physiol , vol.150 , Issue.2 , pp. 535-546
    • Vandepoele, K.1    Quimbaya, M.2    Casneuf, T.3    De Veylder, L.4    Peer Van de, Y.5
  • 43
    • 77249100734 scopus 로고    scopus 로고
    • Network inference and network response identification: moving genome-scale data to the next level of biological discovery
    • Veiga D.F.T., Dutta B., Balázsi G. Network inference and network response identification: moving genome-scale data to the next level of biological discovery. Mol BioSyst 2010, 6:469-480.
    • (2010) Mol BioSyst , vol.6 , pp. 469-480
    • Veiga, D.F.T.1    Dutta, B.2    Balázsi, G.3
  • 44
    • 67949112687 scopus 로고    scopus 로고
    • Discovery of cis-elements between Sorghum and Rice using co-expression and evolutionary conservation
    • Wang X., Haberer G., Mayer K.F.X. Discovery of cis-elements between Sorghum and Rice using co-expression and evolutionary conservation. BMC Genomics 2009, 10:284.
    • (2009) BMC Genomics , vol.10 , pp. 284
    • Wang, X.1    Haberer, G.2    Mayer, K.F.X.3
  • 45
    • 0038631908 scopus 로고    scopus 로고
    • In silico identification of metazoan transcriptional regulatory regions
    • Wasserman W.W., Krivan W. In silico identification of metazoan transcriptional regulatory regions. Naturwissenschaften 2003, 90(4):156-166.
    • (2003) Naturwissenschaften , vol.90 , Issue.4 , pp. 156-166
    • Wasserman, W.W.1    Krivan, W.2


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